PDB-2ost: The structure of a bacterial homing endonuclease : I-Ssp6803I

ID or keywords:

Entry

Database: PDB / ID: 2ost

Title

The structure of a bacterial homing endonuclease : I-Ssp6803I

Components

(Synthetic DNA 29 MER) x 2
Putative endonuclease

Keywords

hydrolase/DNA /

protein-DNA complex / restriction enzyme fold / PD-(D/E)-XK motif /

homing endonuclease /

group I intron / hydrolase-DNA COMPLEX

Function / homology

Function and homology information

endonuclease activity /

nucleic acid binding /

metal ion binding
Similarity search - Function

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.1 Å

Authors

Zhao, L. / Bonocora, R.P. / Shub, D.A. / Stoddard, B.L.

Citation

Journal: Embo J. / Year: 2007
Title: The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
Authors: Zhao, L. / Bonocora, R.P. / Shub, D.A. / Stoddard, B.L.

History

Deposition	Feb 6, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Feb 21, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/2ost ftp://data.pdbj.org/pub/pdb/validation_reports/os/2ost	HTTPS FTP

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Related structure data

Similar structure data	2w55-3 4r5g-d 6rhw-d 3lfk-d 2w54-2 2w54-4 2w55-2 2w3r-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

Y: Synthetic DNA 29 MER

Z: Synthetic DNA 29 MER

A: Putative endonuclease

B: Putative endonuclease

C: Putative endonuclease

D: Putative endonuclease

hetero molecules

87.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	143.777, 143.777, 319.179
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	A
6	1	B
7	1	C
8	1	D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ARG	ARG	A	C	3 - 70	4 - 71
2	1	THR	THR	ARG	ARG	B	D	3 - 70	4 - 71
3	1	THR	THR	ARG	ARG	C	E	3 - 70	4 - 71
4	1	THR	THR	ARG	ARG	D	F	3 - 67	4 - 68
5	2	ASP	ASP	LYS	LYS	A	C	87 - 146	88 - 147
6	2	ASP	ASP	LYS	LYS	B	D	87 - 146	88 - 147
7	2	ASP	ASP	LYS	LYS	C	E	87 - 146	88 - 147
8	2	ASP	ASP	LYS	LYS	D	F	87 - 146	88 - 147

Details

The structure of the I-SspI/DNA complex consists of one protein tetramer bound to a single DNA duplex; the crystallographic asymmetric unit contains one copy of this complex .

#1: DNA chain	Synthetic DNA 29 MER Mass: 8969.772 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic construct containing natural homing site of I-SspI6803I
#2: DNA chain	Synthetic DNA 29 MER Mass: 8862.685 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic construct containing natural homing site of I-SspI6803I
#3: Protein	Putative endonuclease / Mass: 17404.945 Da / Num. of mol.: 4 / Mutation: E11Q,F55K,L16M,L21M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q57253
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal

Density Matthews: 4.67 Å³/Da / Density % sol: 73.69 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% to 20% MPD, 100 mM MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	MPD	1	1
2	MES	1	1
3	MPD	1	2

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)	Wavelength
SYNCHROTRON	ALS	5.0.2		1	0.979
SYNCHROTRON	ALS	5.0.2		2	0.965
ROTATING ANODE			RIGAKU RU200	3		1.5418

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Jun 8, 2006
ADSC QUANTUM 315	2	CCD	Aug 25, 2006
RIGAKU RAXIS V	3	IMAGE PLATE	May 8, 2006

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double-crystal, Si(111) liquid N2 cooled	SINGLE WAVELENGTH	M	x-ray	1
2	Double-crystal, Si(111) liquid N2 cooled	SINGLE WAVELENGTH	M	x-ray	1
3	GRAPHITE	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.965	1
3	1.5418	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
7.6	1	10.7	220038	0.083	1.11	3.1	28899	94
9.5	2	6.7	243144	0.152	1.17	3.3	25721	100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
8.4	50	96.5	1	0.041	0.953	7.3
6.67	8.4	97.8	1	0.055	1.115	7.3
5.83	6.67	98.7	1	0.08	1.285	7.6
5.3	5.83	98.5	1	0.074	1.259	7.7
4.92	5.3	99.4	1	0.065	1.193	7.7
4.63	4.92	99.3	1	0.067	1.268	7.8
4.4	4.63	99.5	1	0.067	1.33	7.7
4.21	4.4	99.7	1	0.078	1.247	7.8
4.04	4.21	99.7	1	0.09	1.118	7.8
3.91	4.04	99.9	1	0.11	1.059	7.8
3.78	3.91	99.8	1	0.131	1.126	7.8
3.68	3.78	99.9	1	0.143	1.146	7.8
3.58	3.68	99.9	1	0.157	1.075	7.7
3.49	3.58	99.8	1	0.189	1.036	7.7
3.41	3.49	98.4	1	0.192	1.005	7.5
3.34	3.41	94.7	1	0.184	1.006	7.3
3.27	3.34	87.9	1	0.193	1	7.3
3.21	3.27	78.2	1	0.271	0.931	7.3
3.15	3.21	69.3	1	0.298	0.926	7.6
3.1	3.15	61.4	1	0.374	0.907	7.6
8.94	50	99.7	2	0.038	1.165	8.9
7.1	8.94	100	2	0.051	1.031	9.5
6.21	7.1	100	2	0.082	1.112	9
5.64	6.21	100	2	0.107	1.003	9.3
5.24	5.64	100	2	0.107	1.047	9.4
4.93	5.24	100	2	0.109	1.176	9.6
4.68	4.93	100	2	0.126	1.209	9.7
4.48	4.68	100	2	0.125	1.245	9.7
4.31	4.48	100	2	0.14	1.156	9.6
4.16	4.31	99.8	2	0.181	1.124	9.6
4.03	4.16	100	2	0.234	1.128	9.6
3.91	4.03	100	2	0.3	1.187	9.6
3.81	3.91	99.9	2	0.357	1.298	9.5
3.72	3.81	99.9	2	0.388	1.139	9.5
3.63	3.72	100	2	0.419	1.434	9.4
3.55	3.63	100	2	0.559	1.177	9.5
3.48	3.55	99.9	2	0.587	1.175	9.5
3.42	3.48	99.9	2	0.616	1.297	9.4
3.36	3.42	100	2	0.597	1.182	9.4
3.3	3.36	100	2	0.628	1.147	9.4

Reflection

Resolution: 3.1→160.13 Å / Num. obs: 28899 / % possible obs: 94 % / Redundancy: 7.6 % / R_merge(I) obs: 0.083 / Χ²: 1.111 / Net I/σ(I): 10.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.1-3.15	7.6	0.374	928	0.907	1,2,3	61.4
3.15-3.21	7.6	0.298	1029	0.926	1,2,3	69.3
3.21-3.27	7.3	0.271	1192	0.931	1,2,3	78.2
3.27-3.34	7.3	0.193	1319	1	1,2,3	87.9
3.34-3.41	7.3	0.184	1420	1.006	1,2,3	94.7
3.41-3.49	7.5	0.192	1491	1.005	1,2,3	98.4
3.49-3.58	7.7	0.189	1531	1.036	1,2,3	99.8
3.58-3.68	7.7	0.157	1511	1.075	1,2,3	99.9
3.68-3.78	7.8	0.143	1529	1.146	1,2,3	99.9
3.78-3.91	7.8	0.131	1498	1.126	1,2,3	99.8
3.91-4.04	7.8	0.11	1523	1.059	1,2,3	99.9
4.04-4.21	7.8	0.09	1549	1.118	1,2,3	99.7
4.21-4.4	7.8	0.078	1515	1.247	1,2,3	99.7
4.4-4.63	7.7	0.067	1533	1.33	1,2,3	99.5
4.63-4.92	7.8	0.067	1516	1.268	1,2,3	99.3
4.92-5.3	7.7	0.065	1529	1.193	1,2,3	99.4
5.3-5.83	7.7	0.074	1543	1.259	1,2,3	98.5
5.83-6.67	7.6	0.08	1543	1.285	1,2,3	98.7
6.67-8.4	7.3	0.055	1566	1.115	1,2,3	97.8
8.4-50	7.3	0.041	1634	0.953	1,2,3	96.5

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Phasing

Phasing

Method:

MAD

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-38.362	-15.456	-63.143	SE	71.25	0.74
2	-38.299	-49.252	-50.778	SE	112.21	1.2
3	-33.355	-41.094	-45.778	SE	93.14	1.07
4	-19.776	-34.049	-39.32	SE	140.1	1.28
5	-35.709	-18.056	-67.057	SE	83.37	0.59
6	-28.713	-40.155	-46.549	SE	166.51	1.24
7	-41.981	-24.697	-76.047	SE	90.54	1.12
8	-32.936	-7.045	-58.308	SE	134.88	1.2

Phasing dm

Method: Solvent flattening

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection

Refinement

Method to determine structure:

MAD / Resolution: 3.1→160.13 Å / Cor.coef. F_o:F_c: 0.891 / Cor.coef. F_o:F_c free: 0.845 / SU B: 22.095 / SU ML: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.024 / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.328	1459	5 %	RANDOM
R_work	0.278	-	-	-
obs	0.281	28898	93.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 83.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.44 Å²	0 Å²	0 Å²
2-	-	3.44 Å²	0 Å²
3-	-	-	-6.88 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→160.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4540	1189	2	16	5747

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	5974
X-RAY DIFFRACTION	r_angle_refined_deg	1.889	2.21	8317
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.497	5	561
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.079	23.244	225
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.415	15	803
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.392	15	39
X-RAY DIFFRACTION	r_chiral_restr	0.228	0.2	909
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	4140
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	2776
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	3915
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	227
X-RAY DIFFRACTION	r_metal_ion_refined	0.111	0.2	6
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.148	0.2	52
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.14	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.374	1.5	2857
X-RAY DIFFRACTION	r_mcangle_it	0.682	2	4492
X-RAY DIFFRACTION	r_scbond_it	0.609	3	3964
X-RAY DIFFRACTION	r_scangle_it	1.158	4.5	3825

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	500	MEDIUM POSITIONAL	0.59	0.5
2	B	500	MEDIUM POSITIONAL	0.42	0.5
3	C	500	MEDIUM POSITIONAL	0.58	0.5
4	D	500	MEDIUM POSITIONAL	0.43	0.5
1	A	471	LOOSE POSITIONAL	1.32	5
2	B	471	LOOSE POSITIONAL	1.08	5
3	C	471	LOOSE POSITIONAL	1.23	5
4	D	471	LOOSE POSITIONAL	1.08	5
1	A	500	MEDIUM THERMAL	0.55	2
2	B	500	MEDIUM THERMAL	0.36	2
3	C	500	MEDIUM THERMAL	0.37	2
4	D	500	MEDIUM THERMAL	0.45	2
1	A	471	LOOSE THERMAL	1.31	10
2	B	471	LOOSE THERMAL	0.95	10
3	C	471	LOOSE THERMAL	0.97	10
4	D	471	LOOSE THERMAL	1.12	10

LS refinement shell

Resolution: 3.1→3.183 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.401	78	-
R_work	0.328	1305	-
obs	-	1383	62.58 %

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